Is EBP p.Pro13Arg (c.38C>G) pathogenic?

EBP p.Pro13Arg (c.38C>G) is classified Conflicting classifications of pathogenicity in EBP (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2026-01-05). AlphaMissense: likely pathogenic (0.7973); Ultra-rare (popmax 0.0173%, nfe).

How common is EBP p.Pro13Arg (c.38C>G) in the general population?

EBP p.Pro13Arg (c.38C>G) is ultra-rare (popmax 0.0173%, nfe) (gnomAD).

What do computational predictors say about EBP p.Pro13Arg (c.38C>G)?

AlphaMissense predicts likely pathogenic (score 0.7973) — an in-silico prediction, not a clinical call.

EBP p.Pro13Arg

c.38C>G · rs150034611 · VCV1965021

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.7973 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0173%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7973	likely pathogenic · top 8% in EBP
REVEL	0.949	strongly pathogenic-leaning
SaProt	LLR -15.88	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2, phastCons 1
Overall
CADD	26.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0173% European (non-Finnish) · 155/893,858 alleles

Filtering AF 0.0151% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0143%

Overall 0.0136% 164/1,205,503 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0173%	5,767
Finnishnot grpmax-eligible	0.00651%	15,357
Remaining individualsnot grpmax-eligible	0.00632%	15,826
Ashkenazi Jewishnot grpmax-eligible	0.00455%	21,991
African / African-American	0.00358%	27,961

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: EBP
Protein: p.Pro13Arg
Coding: c.38C>G
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs150034611
Type: single nucleotide variant
Location: chrX:48523809 (GRCh38)
Structure: AlphaFold pLDDT 59.09

Full EBP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same type
EBP p.Arg110Ter Pathogenic ★★ same type
EBP p.Arg147Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
EBP p.Arg147His Pathogenic ★★ ⚠ same type
EBP p.Arg62Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
EBP p.Glu80Lys Pathogenic/Likely pathogenic ★★ same type
EBP p.Gly161Arg Likely pathogenic ★★ same type
EBP p.Ser98Phe Pathogenic/Likely pathogenic ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ebp-p-pro13arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown